Baboon endogenous type C leukemia viral DNA intermediates have been purified from cells acutely infected withe the virus. The circular viral DNAs were linearized by digestion with the restriction endonuclease EcoR1 and the linearized DNA was molecularly cloned in bacteriophage lambda by recombinant DNA techniques. To prepare specific probes for subgenomic fragments of viral DNA, the full length cloned DNA was restricted into 5 fragments and each of the fragments were independently cloned in the plasmid PBR 322. The organization of the endogenous genetically transmitted viral sequence in baboon DNA and the exogenous horizontally transmitted sequence acquired upon horizontal infection of human and dog cells were compared by Southern blotting procedure. The genetically transmitted sequences and the sequences acquired upon infection showed organizations similar to the DNA of the infectious virus. However, the DNA from virus infected cells (horizontally transmitted sequences) are infectious in DNA transfection assays but the DNA from baboons (genetically transmitted sequences) are 2 to 3 logs less infectious. The factors that potentially regulate viral gene expression are under investigation.